Double Check your paths, and its also important when compiling a map that you have no custom skins, maps, or other extras in your main, mainta, or maintt folder.
In the past I have forgotten to remove custom skin pk3 files and for the longest time couldn't figure out why my map wouldn't compile
Thanks mate, you made my day
That's odd that custom textures would prevent the compile.
It's more of a rule of thumb to removed other pk3's just so you don't accidentally use any textures found in a custom pk3 then compile and pack your map without that (or those) textures.
As I often work on a couple of maps at the same time, I have forgotten that number 1 rule (to remove pk3's) several times but it hasn't prevented the compile.
Same with many others that have released map ".bsp"s with missing textures.
It's because there is a hard-coded limit of shaders that the compiler can read. If you have an excess amount of custom shader scripts it'll fail.